Bio Chapter 5

==The Molecules of Life==

• All living things are made up of carbohydrates, proteins, lipids, nucleic acids
• %%Macromolecules%%: Complex and large molecules
  • Function/properties derive from the order and number of atoms
• %%Polymer%%: Long molecule consisting of repeating building blocks that form long chains
  • Including proteins, nucleic acid, and carbohydrates
  • Fats do not have repeating building blocks
• %%Monomer%%: The units/building blocks make up polymers.

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==The Synthesis and Breakdown of Polymers ==

• %%Enzymes:%% specialized macromolecules that aid in “speeding up” reactions such as those that make or break down polymers.
  • Doesn’t literally speed up the process, it just decreases the amount of energy required to initiate the reaction.
• %%Dehydration synthesis:%% This occurs when two monomers bond together through the loss of a water molecule.
• %%Hydrolysis:%% Using pressure to break the bond and adding a water molecule to the free bonds.
  • Disassembles polymers
  • Without water, those empty bonds can virtually bond with anything else and potentially become poison.

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==The Diversity of Polymers ==

• Variety is created by slightly modifying polymers (from a small set of monomers)
  • Ex. Glycogen is broken down into the cell for energy and the starch is stored as fat
• Least to greatest variety = within the same species vs. between species

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==Carbohydrates & Sugars==

• Carbohydrates include sugars and can vary from monosaccharides (simple sugars) to polysaccharides (macromolecules, composed of many sugar building blocks)
• Almost everything in the body can be broken down to make carbohydrates
• Most common sugar = glucose (C6H12O6)
• Distinct in the position of the carbonyl (as aldose or ketose) and the number of carbons
  • In multiples of CH2O
• Visually, alpha and beta glucose only physically differentiate based on how they react in water
• %%Aldoses:%% Aldehyde sugars
• %%Ketoses:%% Ketone sugars
• %%Trioses:%% 3 carbon sugers (C3H6O3)
• %%Pentoses:%% 5 carbon sugars (C5H10O5)
• %%Hexoses:%% 6 carbon suagrs (C6H12O6)
• ^^In alpha glucose:^^ 3rd carbon is the switch, but the 4th carbon is what changes between glucose and ^^galactose^^ (flipped), on first carbon - hydrogen is up, (aldose on 1).
• ^^In beta glucose:^^ 3rd carbon switch, but 1st carbon is what changes between alpha and beta glucose
• ^^In fructose:^^ 5 carbons (#1 is the Ch2OH) with OH bonded to it, switch on 4, ends with CH2OH bonded with H (Ketose on 2nd)
• ^^Maltose:^^ alpha glucose + alpha glucose
• ^^Sucrose:^^ alpha glucose + fructose
• ^^Lactose:^^ alpha glucose + galactose
• In aqueous solutions, many sugars form rings
• Monosaccharides serve as a major fuel for cells and as raw material for building molecules
• %%Disaccharide (oligosaccharide)%%: Occurs when two monosaccharides bond together from dehydration synthesis (this bond = glycosidic linkage = not an ether bond)
  • Not a polymer
• %%Glycosidic bonds:%% covalent bonds that bond monosaccharides together to form a disaccharide, oligosaccharide, or polysaccharide.
  • Alpha: Below the plane (parallel)
  • Beta: Above the plane (zigzag)
• %%Trisaccharide:%% a polymer and a polysaccharide
  • @@Alpha bonds:@@ :] (direct bonding)
  • @@Beta bonds:@@ :> (zig zag bonding, alternating pattern between molecules)

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==Polysaccharides==

• %%Polysaccharides%%: Contain a large number of monosaccharide units bonded to each other by a series of glycosidic bonds

  • The polymers of sugar have storage and structural roles

• Artificial sugar is bigger = increased chances of clots

• Constant sugar consumption = sugar molecules scratches against capillaries (forms scabs in blood vessels)

• Structure and function are dictated by the number of atoms (monomers) and placements of its glycosidic linkages

• ^^Storage:^^

  • %%Starch%% (Storage polysaccharide for plants): Has storage for glucose monomers (plant version of glycogen)
  • Surplus starch stored in chloroplasts and other plastids
  • The simplest form is amylose
  • %%Glycogen%% (Storage polysaccharide for animals): Has storage for glycogen in liver and muscle cells
  • Hydrolysis of glycogen in these cells releases glucose when there is a sugar demand
  • Has much more branches than starch because it must be easily compressed into cells
  • Cellulose has beta bonds

• ^^Structure^^:

  • The polysaccharide %%cellulose%% = a major component of the tough wall of plant cells
  • Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ
  • The difference is based on two ring forms for glucose: alpha (α) and beta (β)
  • Ex. hard shell of a bug
  • %%Chitin%%: found in the exoskeleton of arthropods
  • Also provides structural support for the cell walls of fungi (why it’s chewy)

• ^^Differences:^^

  • Structural polysaccharides are made up of beta glucose monomers (beta glycosidic linkages), whereas storage polysaccharides have alpha glucose monomers (alpha glycosidic linkages)
  • Starch (alpha config.) is helical (spiral)
  • Cellulose (beta config.) is straight and unbranched
  • Certain hydroxyl groups on cellulose monomers can hydrogen-bond with hydrogen on parallel cellulose monomers
  • Enzymes that digest starch by hydrolyzing alpha linkages cannot hydrolyze beta linkages of cellulose
  • Cellulose in human food passes by the digestive tract as “insoluble fiber”
  • Some microbes digest cellulose and form symbiotic relationships with other animals (ex. cows)

• *Individual glucose molecules are macromolecules, but not polysaccharides

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==Lipids==

• Lipids are the one class of large biological molecules that do not include true polymers
  • Not considered polymers (polymers are different from polysaccharides, which are specific to sugar)
• The unifying feature of lipids is that they mix poorly, if at all, with water
• Lipids consist mostly of hydrocarbon regions
• The most biologically important lipids are fats, phospholipids, and steroids
• Good fats have at least 1 double bond (liquid in room temp)

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==Fats==

• Constructed from fatty acids and glycerol

  • %%Glycerol:%% 3-carbon alcohol with a hydroxyl group attached to every carbon
  • %%Fatty acid:%% Carboxyl group attached to a long carbon skeleton

• Forming as ester linkage = %%esterfication%% (-COO)

• Separates from water because water molecules hydrogen-bond to each other, which excludes the fats

  • Fats separate from water immediately

• In a fat, 3 fatty acids are joined to a glycerol by an ester linkage, creating a triacyglycerol, or triglyceride

• The fatty acids in a fat can be all the same or of 2 or 3 diff kinds

• Fatty acids vary in length (number of carbons) and the number and locations of double bonds

• %%Unsaturated fatty acids%% have more than one double bond (1+)

  • In unsaturated fat = the flat part (cis-double bond) is not all bonded to hydrogens (can be bonded to anything)
  • Fats made from unsaturated fatty acids are called unsaturated fats or oils and are liquid at room temperature
  • In the structural formula, the zigzag is saturated, and the zigzag with a flat part is unsaturated.
  • More than 1 double-bond = polyunsaturated lipids (v healthy)
  • Plant fats and fish fats are usually unsaturated

• %%Saturated fats%%

  • Made from fats with saturated fatty acids and are solid at room temperature
  • Most animal fats are saturated
  • Healthy in small quantities
  • A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits
    Including genetics, bodily systems, habits, etc. Not just saturated fats.
  • ^^Hydrogenation:^^ The process of converting unsaturated fats to saturated fats by adding hydrogen
  • Hydrogenating vegetable oils also creates unsaturated fats with trans-double bonds
  • These trans-fats may contribute more than saturated fats to cardiovascular disease

• Hydrogen or OH on carbon will switch sides under pressure/heat and become a trans fat (body does not like this structure)

• To become a trans fat, the fat must be unsaturated for the double bond

• Major function of fats is energy storage

• Humans and other animals store their long-term food reserves in adipose cells

• Adipose tissue (fat tissue) also cushions vital organs and insulates the body

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==Phospholipids ==

• Two fatty acids and a phospholipid are attached to a glycerol

  • Fatty acids are hydrophobic, but phospholipid and its attachments form a hydrophilic head
  • Choline, phosphate, glycerol

• Charged head bonds with other things

• Bent leg is unsaturated, straight is saturated so that they stay together but still allow different molecules to go ther (both straight = too tight, both bent = too loose and has no protected layer)

• If both legs were straight, it would take A LOT of energy to break apart or multiply

• Phospholipids added to water self-assemble into double-layered sheets called a bilayer

• ^^Surface of a cell:^^

  • Phospholipids are arranged in a bilayer, with the hydorphobic tails pointed towards the interior
  • Phospholipid bilayer forms a boundary between the cell and its external environment

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==Steroids==

• Lipids characterized by a carbon skeleton consisting of four fused rings

• %%Cholesterol:%% prevalent in animal cell membranes and a precursor to which other steroids are synthesized

• High level may cause cardiovascular disease

• Steroid backbone (4 fused rings, one with a double-bond and one as a pentagon)

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==Protein==

• Account for 50%+ dry mass of most cells
  • Responsible for cellular communication, immune system (antibodies specific towards each antigen), and movement, storage, structural support, transportation
• All proteins (when not needed) will be broken down into urea
  • They appear to “speed up” chemical reactions because they reduce the amount of input energy required to kick start the reaction
• Always 1 less water molecule than sugar molecules bonded together (in starch)
• %%Types of Proteins:%%
  • ^^Enzymatic Proteins^^
  • Selective acceleration of chemical reactions
  • Ex. Catalyzing the breakdown of food molecules
  • ^^Defensive Proteins^^
  • Protection against disease
  • Ex. Antibodies help destroy viruses and bacteria
  • ^^Storage Proteins^^
  • Storage of amino acids
  • Ex. Casein, protein of milk.
  • ^^Transport Proteins^^
  • Transport substances
  • May need energy for transport
  • Ex. Hemoglobin
  • ^^Hormonal Proteins^^
  • Coordination of an organism’s activities
  • Ex. Insulin regulates blood sugar concentrations (by opening channels for sugar to enter cells)
  • ^^Receptor Proteins^^
  • Response of cell to chemical stimuli
  • Ex. Receptors in nerve cells detect signals from other nerve cells
  • ^^Contractile and motor Proteins^^
  • Movement
  • Ex. Actin and myosin are responsible for the contracting and relaxing of muscles
  • ^^Structural Proteins^^
  • Support & keep us moving (connective tissue)
  • Keratin in hair or silk fibers in spider webs
• Enzymes act as biological catalysts that reduce the activation energy for chemical reactions
  • Can be used over and over again
• Proteins are all constructed from the same amino acids
• %%Polypeptide:%% Unbranched polymer of amino acid built from those amino acids (DNA will tell protein to make them a certain way)
• %%Protein%%: A biologically functioning molecule that contains one or more of those polypeptides

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==Amino Acid Monomers ==

• Organic molecules with animo group and carboxyl group
• Differ because of differing R groups:
  • Polar side chains (hydrophilic)
  • Electrically charged side chains (hydrophilic)
  • Acid
  • Base
  • Non-polar side chains (hydrophobic)
• Amino acids have peptide bonds
  • Different monomers are bonded with dehydration synthesis
• Polypeptide: polymer of amino acids
  • Can range from a few - 1000+ monomers
  • Have a carboxyl end/c-terminus (COOH) and an amino end/n-terminus (NH2)

==Protein Structure and Function==

• The activity comes from its specific architecture (sequence of amino acid)
  • Polypeptides are specifically coiled, twisted, folded etc.
• The peptide bond must form immediately or else the amino acid will be broken apart or recycled
• The function of a protein usually depends on its ability to recognize and bond to other some other molecule

%%4 Levels of Protein Structure:%%

• ^^Primary^^
  • The unique sequence of amino acids
  • Determined by inherited genetic information
  • DNA → RNA → Polypeptides (give us our unique characteristics)
• ^^Secondary^^
  • Found in most proteins - folds and coils in the polypeptide chain
  • Caused by hydrogen bonds between the repeating components of the polypeptide backbone
  • Can have alpha helix and beta pleated sheets held loosely together
• ^^Tertiary^^
  • Interactions among various side chains (R groups) cause the shape instead of the backbone interactions
  • R group interactions: hydrogen bonds, ionic bonds, hydrophobic interactions, LDF
  • Strong covalent bonds (disulfide bridges) may reinforce the protein’s structure
  • Proteins must be at least at this stage
  • More compressed together
• ^^Quaternary^^
  • Consists of multiple polypeptide chains (2+ form one macromolecule)
  • Ex. Collagen (3 polypeptide ropes), Hemoglobin (2 alpha and 2 beta subunits)
  • Combinations of tertiary structures
• Like high school grades (+ interactions, qualities per grade)
• Structure Changes are caused by:
  • Changed primary structure
  • TEMPERATURE
  • PH
  • Salt concentrations
  • Differing physical or chemical conditions
• Changed protein shape and function = denaturation (biologically inactive)
• Proteins can revert to their original form and purpose when placed back into ideal environments

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==Diseases and Protein Folding==

• %%Sickle Cell Disease: A Change in primary Structure%%
  • A slight change in the protein’s primary structure can change its form and function
  • Sickle cell disease comes from a changed amino acid in Hemoglobin
  • Red blood cells aggregate (combine) into chains and deform into a sickle-shape
  • Normally, the proteins remain independent, but in this disease, they stick together to form a chain which reduces the transportation of oxygen
  • On the 6th amino acid Glu → Val
• Hard to predict a protein’s structure from the primary structure (usually go through various stages before becoming stable)
  • Alzheimer’s, Parkinson’s, etc.

==Nucleic Acids==

• Store, transmit, express hereditary information
• Has carboxyls, amino acid sequence in polypeptide is programmed by the gene
• Genes consist of DNA (a nucleic acid w/ nucleotide monomers)
• %%2 types of nucleic acids%%
  • DNA
  • Directs its own creation
  • Directs the creation of mRNA, and therefore controls protein synthesis
  • RNA
  • Dominant part of DNA is copied to make RNA
• Ribosomes make and are proteins
• This is gene expression
  • Recessive is coiled tightly so that its data is not replicated
  • Dominant genes unwind so that they can be easily replicated and expressed
• ^^Stages of Synthesis:^^
  • Synthesis of mRNA
  • mRNA made out of freed bases in the nucleus (DNA code determines code of RNA)
  • mRNA exits nucleus
  • Movement of mRNA in cytoplasm
  • Ribosome takes mRNA and reads the code
  • tRNA brings amino acids read from the “recipe” to the ribosome
  • Synthesis of Protein
  • tRNA carries amino acids to ribosomes
  • A chain of amino acids is formed
  • Protein is formed out of amino acids
• mRNA = brings info from DNA to cytoplasm 
• tRNA = type or RNA that has 1 particular amino acid to it (drop off the correct amino acid to form polypeptide chains)
  • Amino acids connected to tRNA
• rRNA = specifically makes ribosomes from ribosomes
• RNA = kinda like recipes read to make stuff

Each gene along a DNA molecule directs the synthesis of mRNA

• mRNA interacts with protein-synthesizing machinery in the cell to form polypeptides
• Flow of genetic information = DNA → RNA → polypeptides (protein)

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==Components of Nucleic Acids==

• Nucleic acids = polymers called polynucleotides
• Each polynucleotide is made of monomers called nucleotides
  • Free-floating = 3 phosphate group
  • Part of a DNA = 1 phosphate group
  • Other 2 are used to fuel the combining of nucleotides
• Nitrogenous base, pentose sugar, and phosphate group
• The portion of a nucleotide without the phosphate group (so just sugar and nitrogenous base) is called the ^^nucleoside^^
• %%Nitrogenous bases:%%
  • Pyrimidines (cytosine, thymine, uracil - “y am i single?”)
  • Thymine is only in DNA because of the amino acid code
  • Uracil is only n RNA
  • Has a 6 membered rings (single)
  • Backbone = phosphodiester bond (2 ester bonds with phosphate group)
  • Purines (adenosine, guanine)
  • Has a 6 membered rings fused into a 5 membered ring (double)
  • A double bond with T, C triple bond with G
• DNA has deoxyribose sugar, RNA has ribose

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==Nucleotide Polymers==

• Nucleotides are linked by a phosphodiester linkage to make a polynucleotide
• Phosphodiester linkage = a bond that bonds the sugars of 2 nucleotides
  • Created a sugar backbone unit with nitrogenous bases as appendages
  • Sequence for DNA or mRNA polymer is unique for each gene
• DNA:
  • Double-helix
  • One side of the strand is gene
  • Labeled 5’ and 3’ on opposite ends (phosphate and hydroxyl respectively)
  • A-T and C-G make it possible for identical copies of each DNA molecule to be made when a cell is preparing to divide
• RNA:
  • Single-stranded
  • Complementary pairing can still occur (if the RNA is folded in on itself)
  • Thymine is replaced by uracil, so A and U pair together

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==Genomics and proteomics have transformed biological inquiry and applications==

• Biologists wanted to “decode” genes by looking at their base sequences
• Developed sequencing methods from Human Genome Project

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